Transport refrigeration systems (“TRS”s) are used to cool a container (typically referred to as a refrigerated transport unit or “TU”). The TU can be used to transport perishable items such as produce and meat products. In such a case, the TRS can be used to condition the air inside a cargo space of the TU, thereby maintaining desired temperature and humidity during transportation or storage. Different perishable items can require different desired temperatures during transport. A TRU is attached to the TU to facilitate a heat exchange between the air inside the cargo space and the air outside of the TU. Some TRUs have a compressor which is directly coupled to an engine (e.g., the engine of a vehicle connected to the TU). The engine coupled to the compressor transfers power to the compressor to provide cooling or heating capacity to the TU (e.g., to the volume of space inside the TU). Generally, the engine provides the compressor with two operation modes: (1) a low speed operation mode, and (2) a high speed operation mode. The low speed operation mode is used to control the temperature when the TU has reached a setpoint temperature (e.g., desired temperature) and thus requires low refrigeration system capacity. The high speed operation mode is used during pull-down or pull-up situations when the TU is far away from the setpoint temperature, and thus higher refrigeration system capacity is necessary to change the temperature of the TU to the setpoint temperature. The engine uses more fuel when the compressor is operating in the high speed operation mode than operating in the low speed operation mode. Generally, when the TRS is in operation, the TU can switch between the two discrete speed operation modes (i.e., the low speed operation mode and the high speed operation mode) several times based on the setpoint temperature and the temperature of the TU because the temperature of the TU can change due to the ambient temperature changes and other factors.